Engineering protein-based machines to emulate key steps of metabolism (biological energy conversion)

Abstract

Metabolism is the conversion of available energy sources to those energy forms required for sustaining and propagating living organisms; this is simply biological energy conversion. Proteins are the machines of metabolism; they are the engines of motility and the other machines that interconvert energy forms not involving motion. Accordingly, metabolic engineering becomes the use of natural protein‐based machines for the good of society. In addition, metabolic engineering can utilize the principles, whereby proteins function, to design new protein‐based machines to fulfill roles for society that proteins have never been called upon throughout evolution to fulfill. This article presents arguments for a universal mechanism whereby proteins perform their diverse energy conversions; it begins with background information, and then asserts a set of five axioms for protein folding, assembly, and function and for protein engineering. The key process is the hydrophobic folding and assembly transition exhibited by properly balanced amphiphilic protein sequences. The fundamental molecular process is the competition for hydration between hydrophobic and polar, e.g., charged, residues. This competition determines Tt, the onset temperature for the hydrophobic folding and assembly transition, Nhh, the numbers of waters of hydrophobic hydration, and the pKa of ionizable functions. Reported acid‐base titrations and pH dependence of microwave dielectric relaxation data simultaneously demonstrate the interdependence of Tt, Nhh and the pKa using a series of microbially prepared protein‐based poly(30mers) with one glutamic acid residue per 30mer and with an increasing number of more hydrophobic phenylalanine residues replacing valine residues. Also, reduction of nicotinamides and flavins is shown to lower Tt, i.e., to increase hydrophobicity. Furthermore, the argument is presented, and related to an extended Henderson‐Hasselbalch equation, wherein reduction of nicotinamides represents an increase in hydrophobicity and resulting hydrophobic‐induced pKa shifts become the basis for understanding a primary energy conversion (proton transport) process of mitochondria. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:175–190, 1998.

Function of the F1-motor (F1-ATPase) of ATP synthase by apolar–polar repulsion through internal interfacial water

“…Also significant data to be noted, but not discussed, is microwave dielectric relaxation that allows direct estimates of the numbers of water molecules involved in hydrophobic hydration and demonstrates the competition for hydration by the loss of hydrophobic hydration as carboxyls (eCOOH) ionize to form charged carboxylates (eCOO ÿ ) (Urry et al, , 1998. Microwave dielectric relaxation provides direct experimental demonstration of the competition for hydration between charged and hydrophobic groups that results in DG ap , which is proposed here to provide the force for ATP synthesis and for driving rotation of the g-subunit during hydrolysis.…”

“…As listed below, one specific set of designed model proteins, prepared both chemically and microbially, begins with Model Protein I, having an f V of 0.83 and an f E of 0.17, and introduces more hydrophobic phenylalanine (Phe, F) residues in place of less hydrophobic valine (Val, V) residues (Urry, 1997(Urry, , 2006Urry et al, 1998) to give: with n the Hill coefficient, and pK a given for each member of the series as Phe (F) residues stepwise replace Val (V) residues. The results of increasing polymer hydrophobicity, under conditions of negligible charge-charge interactions (Urry, 1997), are systematic increases in pK a shifts and increased positive cooperativity as evidenced by increases in the Hill coefficient.…”

Batch production of a silk-elastin-like protein in E. coli BL21(DE3): key parameters for optimisation

“…They are adapted from proteins, or more specifically, their amino acid sequences are most typically based on the highly repetitive amino acid sequence blocks of naturally occurring fibrous proteins such as elastin, silk, collagen and/or keratin [1-4]. These repetitive sequences dictate the structure and properties of these materials and are of much interest in the fields of polymer and materials sciences as they offer an exceptional opportunity for the production of polymeric materials in which structure and function are precisely controlled.…”

Elastin-Like Protein, with Statherin Derived Peptide, Controls Fluorapatite Formation and Morphology

“…ELPs are known to have thermoresponsive properties, attributed to their ITT (Urry et al, 1998). It is known that below the ITT the protein is unfolded, mostly with a random coil structure, and the hydrophobic residues are hydrated with clathrate-like water structures (Rodriguez-Cabello, 2004).…”